The human intestine is thought to be sterile in utero, but is exposed to a large variety of maternal and environmental microbes immediately after birth. Thereafter, a dynamic period of microbial colonization and succession occurs which is influenced by factors such as delivery mode, environment, diet and host genotype, all of which impact upon the composition of the gut microbiota, particularly during early life. Subsequently, the microbiota stabilizes and becomes adult-like (Spor, Koren & Ley 2011). The human gut microbiota contains more than 500-1000 different phylotypes belonging essentially to two major bacterial divisions, the Bacteroidetes and the Firmicutes (Eckburg et al. 2005). The successful symbiotic relationships arising from bacterial colonization of the human gut have yielded a wide variety of metabolic, structural, protective and other beneficial functions. The enhanced metabolic activities of the colonized gut ensure that otherwise indigestible dietary components are degraded with release of byproducts providing an important nutrient source for the host. Similarly, the immunological importance of the gut microbiota is well-recognized and is exemplified in germfree animals which have an impaired immune system that is functionally reconstituted following the introduction of commensal bacteria (Macpherson et al. 2001, Macpherson, Martinic & Harris 2002, Mazmanian et al. 2005).
In sharp contrast to the production of secretory intestinal IgA, which is influenced by microbial colonization per se (Chung, Kasper 2010, Macpherson 2006), T cell development and differentiation seem to require colonization by specific commensal micro-organisms. Clostridium species, and in particular the spore-forming segmented filamentous bacteria (SFB), appear to be a potent stimulus for the differentiation and maturation of intestinal and colonic Th1, Th17 and Tregs (Gaboriau-Routhiau et al. 2009, Ivanov et al. 2009). Recent studies have now demonstrated that other gut bacteria, including those of Clostridium clusters IV and XIVa and the Altered Schaedler Flora (ASF), can induce de novo generation of Tregs while mono-colonization with Bacteroides fragilis can correct the Th1/Th2 imbalance in germfree mice by promoting the expansion of Tregs (Mazmanian et al. 2005, Geuking et al. 2011, Atarashi et al. 2011). These data infer important immune-regulatory effects of other resident gut bacteria. Clearly, the effects of commensal bacteria on T cell differentiation pathways is variable and as postulated previously may be influenced by the array of TLR ligands found associated with specific bacteria (Nutsch, Hsieh 2012). For example, the mechanism by which SFB influences T cell responses is currently unknown, but recent genome studies confirming the presence of flagellin genes suggest that innate responses mediated through TLR5-flagellin interactions may be important (Prakash et al. 2011, Sczesnak et al. 2011). Furthermore, the Treg-enhancing effects of B. fragilis have been linked with PSA and mediation by TLR2 signalling events (Round et al. 2011).
Dramatic changes in microbiota composition have been documented in gastrointestinal disorders such as inflammatory bowel disease (IBD). For example, the levels of Clostridium cluster XIVa bacteria are reduced in IBD patients whilst numbers of E. coli are increased, suggesting a shift in the balance of symbionts and pathobionts within the gut (Frank et al. 2007, Scanlan et al. 2006, Kang et al. 2010, Machiels K. et al. 2013). Interestingly, this microbial dysbiosis is also associated with imbalances in T effector cell populations.
Roseburia belongs to the phylogenetic cluster XIVa of the Firmicutes phylum. Currently, within the Roseburia genus, five species have been identified and characterised: Roseburia cecicola, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans (Stanton and Savage 1983, Duncan et al 2006). The bacteria are flagellated commensal anaerobes and are also major butyrate producers (Duncan et al. 2006). Although precise numbers of these bacteria colonizing the human gut have not been accurately estimated, Roseburia spp. are dominant in the healthy human gut and are under-represented in IBD patients (Machiels K. et al. 2013).
The roles of bacterial genes, in particular flagellin, participating in colonization and adaptation to the murine gut, as well as the host immune genes responding to colonization by Roseburia bacteria are disclosed. The inventors show that specific flagellin structures of Roseburia such as R. hominis and R. intestinalis induce distinct signalling responses in both epithelial cells and dendritic cells relative to other flagellate enteric bacteria. The importance of the TLR5-Roseburia, such as TLR5-R. hominis, interactions in directing the host adaptive response, in particular Treg responses is demonstrated. The complete genome sequence and annotation for R. hominis described herein is shown in GenBank under accession number CP003040 (version 1). For R. intestinalis (GenBank Accession Number for 16S rRNA gene strain L1-82: AJ312385) described herein the reference genome sequence is shown in GenBank under accession number ABYJ02000000 (version 2) and consists of sequences ABYJ02000001-ABYJ02000409.